There are various reasons why files on a hard disk may not be properly accessible. Here are some reasons and ways to identify and address each in OS X.

Unifying logical and physical access is a step that you probably need to take to address these issues and standards can help. Standards: From Where and Why Technology lives and dies by standards.

A logical database can stretch over multiple physical hard disks and information files. The data storage unit is still a single database for information retrieval purposes.